Re: 1-5 Intramolecular repulsions

From: rocwhite168 (
Date: Wed Nov 05 2014 - 13:02:55 CST

HI Kenno,

In some force fields hydrogen atoms are modeled by a single positive
point charge without LJ potentials. This will create difficulty in
molecules like 1,2-diols, because hydrogen in a OH group will want to
be on top of oxygen in the neighboring OH group. Adding a special 1,5
repulsion term helps solve the problem. Similar issues exist for TIP4P
model, for example, if you run GCMC or GEMC.



On Wed, Nov 5, 2014 at 12:33 PM, Kenno Vanommeslaeghe
<> wrote:
> While the answer is in all likelihood "no", the question is poorly
> formulated; I read it a few times over and I'm still confused about what
> exactly you're looking for (and I work on force fields on a daily basis). Do
> you mean "exceptions" instead of "interactions"? Also, if you want an R^-12
> repulsion without R^-6 attraction (which raises questions about the
> rationale behind the force field), you also have to worry about whether NAMD
> lets you specify them separately (I honestly don't know). Finally, your "for
> example" link doesn't work; it likely relies on form data that is not
> contained in the URL.
> On 11/05/2014 12:54 PM, Rebecca Lindsey wrote:
>> Dear All,
>> Is there a way to include 1-5 (intramolecular) interactions in NAMD? As
>> far as I understand, neither NBFIX nor NBTABLE can be used to accomplish
>> this, as do not allow for a distinction between intra- and inter-molecular
>> interactions.
>> The repulsion term in question would be along the lines of: E_repel =
>> a_repel/(r_ij)^12, as it is given by the TraPPE force field. (see, for
>> example:
>> Thanks in advance for your insights.
>> --
>> Rebecca K. Lindsey
>> ----------------------------------------------------
>> Ph. D. Candidate Website <>
>> University of Minnesota LinkedIn
>> <>
>> Twin Cities <>
>> UMN Chemical Theory Center <>
>> ----------------------------------------------------

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